15-December-2009

CCDC Archives 500,000th Crystal Structure

The Cambridge Crystallographic Data Centre (CCDC) has announced an important milestone in the
history of crystallography--the archiving of the 500,000th small molecule crystal structure to
the Cambridge Structural Database (CSD). For more information, visit the CCDC at
www.ccdc.cam.ac.uk.

Use Widgets to Embed RCSB PDB Features on Your Website

Molecule of the Month images and text, static images and interactive views for any PDB structure, and
RCSB PDB searches based on ID, keyword, or author name can be embedded into any website using the RCSB PDB's web widgets.
These small bits of code can be customized to display and link to RCSB PDB features.

* The RCSB PDB Molecule of the Month widget embeds an image from the feature and links to the entire article.
The widget can be customized to specify width, colors, amount of text shown, and molecule.

The 'simple' widget version displaying the May 2003 Molecule of the Month

* The Tag Library can be used to embed an image that links to the corresponding Structure Summary page;
provide a menu of links to a particular entry's Jmol view, Structure Summary Page, and PDB file;
and provide a link that performs a current keyword query.

Several structures of the whole tobacco mosaic virus are available in the PDB, including the
ground-breaking one solved by X-ray fiber diffraction (shown here from PDB entry 2tmv

), and
a recent structure solved by analysis of many electron micrographs (PDB entry 2om3). The virus
is composed of one strand of RNA (shown in red) wrapped inside a sheath of protein (shown in blue).
The protein coat is composed of about 2130 copies of a small protein, which stack like bricks
in a cylindrical chimney. The RNA strand encodes four proteins, which together orchestrate the
life cycle of the virus. These include two proteins that replicate the viral RNA, a protein that
transports the RNA from cell to cell, spreading the infection, and the capsid protein
seen in the PDB structures.

(Click
image to enlarge)The structure of rat liver vault at 3.5 angstrom resolution has been split into PDB entries
2ZUO, 2ZV4, and 2ZV5. The Structure Summary page for all of these entries displays an image of the complete composite
structure. Clicking on "View in Jmol" will launch a Jmol display with the composite structure.

08-December-2009

New Feature: Improved Display of Large Structures

Images and Jmol displays on the RCSB PDB website now show the complete biological assembly for all structures--even
for proteins that are split across multiple PDB coordinate files.

A number of structures in the PDB archive are so large that the historical
limitations of the PDB file format (maximum of 99999 atoms and 62 unique chains)
require them to be split across multiple PDB coordinate files. Examples include
extremely large ribosome complexes (e.g., 1GIX, 1GIY), and
structures that contains a very large number of atoms or chains, such as the
vault protein (e.g.,
2ZUO,
2ZV4,
2ZV5).

These structures are identified on Structure Summary pages in the new "Split Entry" box,
which lists and links the PDB IDs of all entries that make up the composite structure.
A link is provided to easily download all of the related coordinate files.

Images on the Structure Summary page now illustrate the full composite structure, rather than
what is found in each individual PDB coordinate file. The image on the Structure
Summary page for 1GIX, for example, shows the full ribosome structure
composed of entries 1GIX and 1GIY. For all Structure Summary images, the forward and backward
buttons can be used to toggle between the asymmetric unit and the biological assembly (or
multiple biological assemblies, if applicable) for the full structure.

The biological assembly and asymmetric unit of the composite structure can be launched in
Jmol when viewing the corresponding static image. The display of such large structures in
Jmol is possible by loading PDB files limited to CA and P atoms, and by using the Jmol
load files command.

See the WHAT'S NEW page to learn about other recently-added features and improvements.

01-December-2009

Upcoming Meetings: ASCB

From December 5-9, the RCSB PDB will be at the 49th Annual Meeting of the American Society for Cell Biology in
San Diego, CA. Stop by exhibition booth 730 to meet with members of the RCSB PDB and the PSI Structural Genomics
Knowledgebase (PSI SGKB). David Goodsell, author of the Molecule of the Month, will discuss "Visual Representation
from Atoms to Cells: New Work from the Machinery of Life" as part of a session on Exploring Cell Biology at the
Frontier of 3D Visualization (Saturday, December 5, Room 15A). The PSI SGKB will be presenting a poster (Sunday,
December 6, board B713) and a tutorial (Monday, December 7, 5:45pm, Room 25A) on the "One-Stop Shop For Protein
Structure, Function, Sequence, Methods, and More."

24-November-2009

(Click
image to enlarge)Prepared and customized reports can be generated for search results.

New Website Features: Improved Tabular Reports

For any search result, users can examine individual PDB entries or review the entire set of
structures by creating reports that can be viewed online or downloaded. Recently,
this reporting system has been enhanced with improved functionality and navigation,
and now offers better support for reporting on very large result sets.

Report Navigation
Reports can be generated for structures matching a query by selecting any of the prepared reports
available from the pulldown menu or by creating a new, customized report. Instead of
presenting the entire report on a single page, reports are now available on multiple,
customizable pages. By default, the first 15 records sorted by PDB ID are shown,
with an option to list more records per page.

The entire table can be sorted by clicking on the column headers. All column widths are
resizable by dragging the line between two columns. Within the reports themselves,
PDB IDs link to that entry's Structure Summary page, PubMed IDs to the abstract,
and Ligand IDs to a Ligand Summary page.

Exporting Reports
Tables can be exported in three formats: Excel 97-2003, Excel 2007 or newer, and CSV, or
Comma Separated Value format (recommended for extra large data sets that may surpass size
limitations in Excel).

Generating Large Reports
A new feature is the ability to generate reports with extremely large sets of data. For
example, a report displaying the X-ray Refinement Details (Rvalue, Rfree, and Resolution)
can be made for all crystal structures in the PDB.

Selecting the number for X-RAY / Total will return the more than
53000
structures that match this query. From the navigation bar,
click on "Generate Reports" and select the report Experimental
Reports >> X-ray >> Refinement. This report can be browsed, formatted, and
downloaded as described above.

Other large reports, such as the summary reports for Biological Details and Sequence,
can be easily generated for all structures in the PDB.

The latest website release also includes enhancements to browsing query results,
viewing large structures, and more. See
the WHAT'S NEW page for detailed descriptions.

Newsletter Published

In the Education Corner, Gary Battle reports on a recent symposium that demonstrated
the different ways the Cambridge Structural Database is used to teach chemistry.
In the Community Focus, Roland Dunbrack, Jr. (Fox Chase Cancer Center) discusses
his research in computational structural biology and the software his laboratory
makes available for download.

10-November-2009

(Click
image to enlarge)The new "Latest Publications" search

Latest Publications: How to Access All Articles in Each Update

Available from the left-hand menu, the new
"Latest
Publications" search returns the PubMed articles associated with PDB structures in the most recent update.
This includes publications for newly released
structures and for
structures whose PubMed abstracts were added to our database in that update.

The results are presented in the Query Results Browser with the "Citations" tab highlighted by default.
The other query results tabs are provided as well, so by clicking on the "Structure Hits" tab,
all structures associated with the publications can be explored.

Clicking on the first icon in the blue bar above the citations (
) downloads all citations in
Medline format.

03-November-2009

DOIs for PDB Structures and the Molecule of the Month

PDB structures can be cited using their PDB ID and the related published citation.

Structures may also be referenced using their Digital Object Identifier (DOI).
These DOIs are formatted as 10.2210/pdbXXXX/pdb - where XXXX is the PDB ID.
For example, the DOI for entry 4HHB is "10.2210/pdb4hhb/pdb".

DOIs are also available for each RCSB PDB Molecule of the Month feature with the format:
10.2210/rcsb_pdb/mom_YYYY_MM (where YYYY is the year, and MM the number of the month, one or two digits).
For example, the DOI for the May 2003 feature on hemoglobin by Shuchismita Dutta and David S. Goodsell is
"10.2210/rcsb_pdb/mom_2003_5".
An RCSB PDB Molecule of the Month feature may be referenced using the DOI and the author/s of the article.

A page describing
policies & references
for using and citing PDB data and RCSB PDB resources is available.

Many thanks to Elspeth Garman (University of Oxford) and Joel Sussman (Weizmann
Institute of Science) for judging the posters, and to Andreas Roodt (University
of the Free State, South Africa) for organizing the judging.

13-October-2009

Nobel Prize Awarded for the Structure of the Ribosome

Three structural biologists have won the 2009 Nobel Prize in Chemistry for studies of the structure and
function of the ribosome -- Venkatraman Ramakrishnan (MRC Laboratory of Molecular Biology),
Thomas A. Steitz (Yale University), and
Ada E. Yonath (Weizmann Institute of Science).
The depositions of their first complete ribosome subunit structures
(1fjg, 1ffk, and
1fka) almost a decade ago ushered structural biology into a new
era. Since that time, more than 120 ribosome structures consisting of 50S, 30S subunits
and complete 70S ribosomes have been contributed by these Nobel scientists. The structures,
complexed with and without antibiotics, tRNAs, mRNAs, initiation factors, and release factors,
provide a basis for understanding how the ribosome works and are useful tools for drug development.

06-October-2009

wwPDB FTP Advisory Notice

The script for mirroring the FTP site using the RSYNC program will be modified to prompt the user to choose one of three rsync servers (RCSB PDB, PDBe, PDBj).

The top-level README file will point to the download instructions hosted on the wwPDB website.

The directory of newsletters will be updated.

Sequence cluster data that is used only by the RCSB PDB website will be removed from the wwPDB FTP site. The data will be made available from the RCSB PDB at
ftp://resources.rcsb.org/sequence/clusters/.
These data are currently at:

22-September-2009

What's New at the RCSB PDB?

The WHAT'S NEW button at the top of the RCSB PDB header highlights
recently-released tools and enhancements to the website. Descriptions, examples, and in some cases, screencasts illustrate how to access and
use these features. Recent examples include new options available for
reviewing query results and the Comparison Tool for calculating
pairwise sequence and structure alignments.

This functionality is also integrated with the Sequence Clusters offered from each entry's Sequence
Similarity tab, for example 4HHB. Users can select a pair of chains from a given sequence cluster (95% for this example),
and then run either sequence or structure alignments.

The current sequence alignments possible are: blast2seq, Needleman-Wunsch, and Smith-Waterman; the structure alignments offered are FATCAT,
Mammoth, TM-Align, and TopMatch. FATCAT alignments can be viewed on the external server at
fatcat.burnham.org/fatcat or through the RCSB PDB's new JFatCat tool.
JFatCat is a 3D structure alignment program based on FATCAT,
BioJava and Jmol. JFatCat can be launched from the
Comparison Tool or downloaded to the desktop.

08-September-2009

Improved Navigation of the RCSB PDB Website

RCSB PDB web pages been reorganized to make navigating the website and search results easier and more intuitive.

The left-hand menu now groups frequently-used webpages into sections -- Deposition, Home, Search, Tools, and
Education -- that can be moved up and down to create a left-hand menu ordered by user interest. This customized
menu will then appear on every webpage. Links that appeared in the old left-hand menu system have been moved
to more contextual places, such as query result pages.

By default, search results now display the most recently-released structure first. Results can also be sorted
by PDB ID, Residue Count, and Resolution.

Query result pages offer different tabs for reviewing any Structure Hits, Unreleased Structures, Citations,
Ligand Hits, Web Page Hits, and GO, SCOP, and CATH Hits. Options for viewing, downloading, and generating
reports for these search results appear as icons at the top of each page. Mousing over the icon indicates
what action will be performed. A detailed description of the new result browser options is available at:

25-August-2009

Beta Release of Redesigned BioSync

New capabilities and descriptions of operational synchrotron beamlines worldwide are now
available at biosync-beta.rutgers.edu.
The new site also offers search functions for services and equipment.
BioSync has been redesigned to
include the dramatic changes in data collection capabilities at synchrotron
beamlines (including remote data collection, mail-in, crystallization and structure
solution services, robotics handling for crystal screening and mounting, microfocus
beams and facilities for collecting data under extreme conditions). The new look and
feel of the website helps users find information about particular beamlines and to
search for capabilities, services and equipment. The website's enhanced interface
lets synchrotron personnel dynamically edit and add data.

BioSync offers deposition statistics by each synchrotron site and by geographical region.
Galleries of structures and tables containing citations and other general information
(e.g. phasing methods, resolution, R-factors, numbers of atoms) are also available.
A separate set of statistical tables, galleries and informational tables is provided
for structures produced by structural genomics efforts.

BioSync was formed in 1990 as a grassroots organization for the promotion of access
to synchrotron radiation for scientists whose primary research was in the field of
structural biology. In 1995, PDB depositions from synchrotron data came from 20
beamlines spread out over 7 different sites, and they accounted for 17% of the total
number of X-ray structures deposited that year. By 2000, there were more than
60 beamlines collecting data on macromolecules and the percentage of X-ray structures
collected on these beamlines was at 62%. This growth in demand was foreseen by the
members of BioSync and they suggested that a web resource be created to help structural
biologists identify beamlines suited to their particular experiments and the BioSync
web resource went online in 2000. By 2009, the number of beamlines used to collect data
on biological macromolecules has more than doubled and they account for close to 80% of
current X-ray structures deposited to the PDB.

18-August-2009

New Opportunities to Solve and Study Protein Structures with PSI:Biology

NIGMS has released three funding opportunities that will establish the core of the PSI:Biology research network,
which will apply high-throughput structural approaches to solve interesting biological problems:

Consortia for High-Throughput Enabled Structural Biology Partnerships:
these awards will support functional studies of proteins proposed by individuals or groups of researchers from across all fields of biology as well as
support the structural determination of those proteins through consortia with the PSI:Biology structure centers. Ideal projects will integrate functional
and structural data for a large number of protein structures to solve significant biological problems.

Additional program announcements for experimental technology development, computational and molecular modeling will be announced.

11-August-2009

Newsletter Published

The summer 2009 issue
(HTML |
PDF)
highlights the new features and functionality that have been added to
www.pdb.org. In the Community Focus, Gregory Warren
discusses the worlds of modeling and crystallography. Recent outreach activities, along with data
deposition and data query news, are also available.

04-August-2009

Turn Your Computer into a PDB Structure Kiosk

Highlight structures from your lab, institution, or class with the
Molecules
in Motion Kiosk Viewer. Using a list of PDB IDs, this full-screen animation program will display any PDB structure from different angles and perspectives.
It also focuses on any chemical components within the structure. The Java viewer can be downloaded or launched
from the Educational Resources page.

21-July-2009

Upcoming Meetings: ACA

From July 25-30, the RCSB PDB will be at the 2009 Meeting of the American
Crystallographic Association in Toronto, Canada. Stop by exhibition booth 418 to meet with members of the RCSB
PDB and the PSI Structural Genomics Knowledgebase (PSI
SGKB). On Tuesday, July 28, the poster "The PDB: Updates and Future Plans" will describe recent improvements made
to the PDB File Format and future plans for a common wwPDB deposition and annotation tool. The
RCSB PDB Poster Prize will be awarded
to the best student presentation related to macromolecular crystallography.

14-July-2009

Upcoming Meetings: Protein Society

At the 23rd Annual Symposium of The Protein
Society (July 25-29, Boston, MA), the RCSB PDB will be exhibiting alongside the PSI Structural Genomics Knowledgebase
(PSI SGKB) in booth #122. On Sunday,
July 26, be sure to stop by the poster A Lot More Than Coordinates: A Short Tour of a PDB File. Presented by
Lihua Tan, this poster will highlight all of the rich information available in a PDB file other than the X, Y, Z coordinates.
Also on Sunday, the PSI SGKB will host a workshop that will describe How to Use the PSI Structural Genomics Knowledgebase
for Research (Salon B, 12:00-1:00 p.m.).

07-July-2009

Sequence Similarity Views of PDB Structures

Interested in finding homologous protein structures, or finding a non-redundant set of proteins?
The new Sequence Similarity View is an easy way to get this information based upon a protein chain
in a PDB entry. This view, available through a tab at the top of each Structure Summary page, provides
clusters of structures at different levels of sequence similarity. Details about the structures of all
homologous proteins found within a cluster can then be examined.

The clusters are based on a weekly BLAST analysis of all proteins with more than 20 amino acids in the PDB.
Many PDB entries contain several chains, so the sequence similarity is defined on a chain-by-chain basis,
with the results returned for the entire structure. For more information, see the description at
http://www.pdb.org/pdb/statistics/clusterStatistics.do.

30-June-2009

wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe

Starting July 1, 2009, Gerard Kleywegt will lead the Protein Data Bank Europe
(PDBe)
project at the European Bioinformatics Institute (Hinxton, UK). During the last
17 years he has been working in Uppsala,
Sweden, a center of excellence for biomolecular crystallography and has developed
many tools that are widely used by structural biologists worldwide. He has an
extensive publication record and has served on the PDBe Scientific Advisory
Board for the last few years. He has also been one of the European
representatives on the wwPDB
advisory committee. He has a very strong international reputation and is well
respected in the structural biology community.

Gerard will be replacing Kim Henrick, who has been the team leader of the
PDBe since 2001. During his tenure at the EBI, Kim has made enormous
contributions to the PDBe at the EBI, by establishing and leading a
strong team that has developed a wide variety of services. Kim was
a strong advocate for the formation of the
wwPDB in 2003. He has played a
key role in developing the standards for representing all the data
in the archive from small molecules to very large biological assemblies,
and in leading the remediation efforts. Kim's deep knowledge of the PDB,
his very critical eye, and sharp wit will be greatly missed by the wwPDB.

The members of the wwPDB
look forward to working closely with Gerard and wish Kim all the best in the next
chapter of his career.

Also at this meeting, the RCSB PDB Poster Prize will be awarded for the outstanding
student poster in the structure and function prediction category. At the ISMB
satellite Bioinformatics Open
Source Conference (BOSC), the RCSB PDB's Andreas Prlić will present BioJava
2009: an Open-Source Framework for Bioinformatics, and at the
BioLink
Special Interest Group Session on the Future of Scientific Publishing, Phil Bourne will
discuss OpenID vs. ResearcherID.

16-June-2009

How does an HPUB structure get released?

An HPUB status indicates that a structure will be released when the primary reference is published. When
it's confirmed that the corresponding article is available, the structure is included in the weekly update of
the PDB.

The wwPDB receives publication dates and citation information directly from a few journals. For most articles,
however, the wwPDB searches PubMed and scans the literature for publication information. Citations
emailed to deposit@wwpdb.org are also greatly appreciated.

There is a one-year limit on the length of a hold period, including HPUBs. If the citation for a structure
is not published within the one-year period, depositors will be given the option to either release or withdraw
the deposition.

02-June-2009

Literature View: Looking at Structures in PubMedCentral

(Click
image to enlarge)

The recently-released Literature View aims to provide a broad look at how a given structure has been analyzed
and presented in open access publications, that is, where the full text of the article is available without
copyright restriction. The overall intent is to make the PDB user more aware of publications associated
with the structure under study. It is one of many new features added to the RCSB PDB website -- a
full list is available.

Accessible by selecting the Literature tab from any Structure Summary page, this view highlights a
variety of published articles associated with a PDB entry. The primary citation's abstract is
included and can be used to search for structures with PubMed abstracts containing the same keywords.
The Literature View also indicates the other publications included in the entry by the authors in
addition to the primary citation (those contained in REMARK 1).

In collaboration with the BioLit project (biolit.ucsd.edu), the Literature View lists any open access articles
found in PubMedCentral that contain the entry's PDB ID including papers that don't include the PDB ID's primary
citation in the references. Links to the abstract and copyright information, along with figures and related
legends from these articles are displayed.

If the listed open access articles also mention other PDB entries, their image, PDB ID, title, and sequence
similarity to the initial structure are included in a table with links to their Structure Summary pages.

To see some examples, explore the Literature View for entries
1TIM,
1O4X,
2G12, and
1AOI.

26-May-2009

Release of new design, features, and functionality

The modernized look of the RCSB PDB website compliments the new features and functionality released this week.
A full "What's New" list for this release is available, with some of the new features highlighted below:

Quick searches by PDB ID/keyword, author name, structural genomics center, and chemical
component name and ID are available from a new pulldown menu offered on every page.

Customizable Structure Summary pages let users highlight particular types of information.
Boxes ("widgets") can be clicked and dragged, and their content hidden or shown.
New layouts are automatically stored for future visits. A video screencast
demonstrates how to customize the layout of this page.

These pages use icons to indicate links to help pages (?), molecular viewers
(),
database searches (),
and external sites ().
Holding your mouse over a search
field or link option will display more information.

The Ligand Explorer Viewer available on the Structure Summary page can be used to
dynamically view hydrogen bond, hydrophobic, bridged H-bond, metal interaction,
and neighbor residue interactions and thresholds.

Other new features include a Literature Tab View that incorporates PubMedCentral
abstracts and images, and a Sequence Similarity Tab View that provides provides an
overview of the sequence clusters for each protein chain in a PDB structure.

19-May-2009

5 Easy Steps for Structure Deposition

Depositors can follow these steps to make the process of depositing a structure quick, easy, and
accurate!

Check the sequence, which should contain all residues used in the experiment, including expression tags
and residues missing due to disorder. Use BLAST1 to determine the appropriate sequence database
references for the proteins or
nucleic acids present in the file. Any sequence mismatches
should correspond to mutation, variant or expression tags in the submitted sequence.

Check the ligands. Ligand Expo can be
used to see if any of the chemical components in the structure (ligands, drugs, inhibitors, ions, modified residues,
etc.) already exist in the Chemical Component Dictionary.
If found, use the corresponding 3-character code in the coordinates; otherwise, the new component can be uploaded in
ADIT along with the structure.

Prepare data for deposition. Use pdb_extract to
automatically collect information needed for deposition from the output files produced by many structure determination
applications, and SF-Tool to convert the structure
factor file format and check the data with SFCHECK.2

Validate the structure with the Validation Suite
and Server to ensure that the data being deposited are accurate and reflect what you intend to submit. This
program checks the sequence and file format consistency, compares geometrical and chemical interactions to
various standards, and reports errors that should be corrected before deposition.

Deposit
using ADIT/ADIT-NMR to
check, validate, and edit the PDB data entries.

Deposition is an iterative process. If you encounter problems at a particular step, please make the correction(s) and
go through the steps again.

These steps, along with a checklist of items needed for deposition, are described in an updated brochure called 5 Easy
Steps for Structure Deposition. For a printed copy or for a packet of information about the deposition process, please
send your postal address to info@rcsb.org.

12-May-2009

Looking at Structures: A Resource for Learning About PDB Data

Where are all the hydrogen atoms in this file? Should I care about the
R-factor? Why are there 20 overlapped structures in my file? These
questions and many others are explored in the RCSB PDB's new
Looking at Structures.

Using text, images, and interactive Jmols, Looking
at Structures intends to help researchers and educators get the most out of the PDB archive. Broad topics include
how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring
the archive.

05-May-2009

Ligand Expo: Searching and Browsing Features

Ligand Expo can be used to access chemical
and structural information about all small molecule components found in PDB entries.

The latest release includes amino acid variants--protonation and de-protonation states--as part of Ligand Expo's
Browse option. For example, when browsing arginine, protonation states ARG_LEO2 and ARG_LFOH_RNH1 will
be included in the results list.

Ligand Expo can also Search for ligands using:

files in a variety of formats including PDB, MOL/SDF and the Refmac/Phenix monomer library (mmCIF)

21-April-2009

Improve the Quality of Your Depositions with SFCheck

SFCheck is integrated with the RCSB PDB's deposition tools so users can assess the agreement between
an atomic model and the corresponding X-ray data before a structure is deposited and released.

SFCheck generates reports containing R-factors, density correlation, Luzzati plots, Wilson
plots, temperature factors, local error estimation by residues, and more. It is a part
of the Validation
Server and ADIT,
and is used by the RCSB PDB during the annotation process.

SFCheck is also part of
SF-Tool, a
streamlined, web-based tool for validating crystallographic experimental data. In addition to
validating model coordinates against structure factor data with SFCheck, SF-Tool can:

14-April-2009

Newsletter Published

In the spring 2009 issue
(HTML |
PDF),
David Goodsell interviews molecular animators Gaël McGill and Graham Johnson to
find out how PDB data gets translated into their detailed movies and images. In the Education Corner,
Gavin Whittaker describes how physical models can be created and used to provide a unique view of molecular
structure. New RCSB PDB features and developments, including the recent release of MyPDB email alerts,
are highlighted.

Exhibition at Experimental Biology

Please stop by the RCSB PDB's exhibition booth at the 2009 Experimental Biology meeting (April 18-22) in New
Orleans, Louisiana. Staff will be available at booth #1410 to answer questions and to demonstrate the many
deposition and query features available from
www.pdb.org.

Do you use protein crystal structure data? Ever wonder why things do not work out as you expect?
Are ligand strain energies unreasonably high? Does your drug candidate not appear to make the hydrogen bonds you expect?
Is that really a water molecule in the corner of a binding site?
Do you wonder why a side chain is in one position rather than another?

These questions all relate to the "quality" of the data you use.
How "good" are the protein structures that you use?
What's the error in atomic coordinates?
How might you know if something is just plain wrong?

Crystallography for Modelers will address these issues and offer
insight into state-of-the-art research into the quality, errors, and "gotchas"
in crystal structure data. Designed by active users of the data, the instructors
are experts from RCSB PDB team members, Rutgers researchers, and commercial
software developers. It is not an introductory course for crystallography
or modeling, but rather a down-and-dirty discussion of crystallographic data,
precision, accuracy, and possible errors.

Registration is for Day 1, Day 2 or both.
Day 2 will expand on Day 1 and offer an opportunity for hands-on learning.

Day 1: The process of crystal structure determination.
Insight into the workings of the PDB and how "PDB" files are generated.
Detailed examination of the extensive information (beyond coordinates)
available in data files and online, including ligand structures.
Proper interpretation of crystal structures, part one: accuracy,
precision, problems and errors (experimental, real, perceived).

Day 2: Proper interpretation of crystal structures, part two:
case studies with emphasis on ligand binding, position, conformation,
loops, and missing density. Software bridging modeling and crystallography.
Hands-on exercises in the concepts of the course with public and commercial
software. Software vendor showcase.

31-March-2009

Bridgewater-Raritan High School Wins New Jersey Science Olympiad Protein Modeling State Finals

After their win at the Central Regional tournament, the team from Bridgewater-Raritan High School came in first place at the protein modeling event at the 2009 New Jersey Science Olympiad.

(Click
image to enlarge) Bridgewater-Raritan HS at the competition.

(Click
image to enlarge) West Windsor Plainsboro South HS.

(Click
image to enlarge) The models were carefully judged by RCSB PDB staff.

(Click
image to enlarge) Livingston High School.

In an extremely close competition, West Windsor-Plainsboro High School South came in second, and
Livingston High School came in third out of 24 schools.

Teams from all over the Garden State submitted their hand-built 3D models of a ribonuclease protein,
along with an abstract, to be judged by staff from the RCSB PDB. At the competition, teams built a
model of a selected region of a ribonuclease structure using Jmol and completed a written exam.
Teams used the Molecule of the Month and other RCSB PDB resources, to help prepare for this event.

Congratulations to all participating teams--there were many great models, abstracts, and responses to the
written exam. The final results, pictures, and a video demonstrating how models are built for this
competition are available at education.pdb.org. Questions about the
NJ Science Olympiad Protein Modeling trial event should be sent to
buildmodels@deposit.rcsb.org.

24-March-2009

RCSB PDB at the San Diego Science Festival April 4

Come build virus models with the RCSB PDB at Expo Day on
April 4th in Balboa Park, San Diego, CA.

As part of the San Diego Science
Festival (SDSF),
Expo Day will offer a full day of hands-on activities for every type of science-enthusiast. In
addition to building viruses, scientists will be on hand at the RCSB PDB booth at the Expo to help
visitors explore the many structures found in the PDB archive. Visitors will also learn the
latest ways to conserve water resources and discover how the cars of tomorrow will mulch vegetable
oil into fuel. Interactive activities, comedians and stage shows will captivate and excite
any aspiring scientist.

SDSF is planned as one of the nation's largest multi-cultural, multi-generational, multi-disciplinary
celebrations of science. It will bring together students, families, businesses, scientists, and
communities for a festival that is interactive and fun, highlighting the impact of science and
innovation on our lives. The Science Festival is hosting FREE activities throughout March
and the beginning of April. On April 1, high school students from all over San Diego County
will visit UCSD for an invited event that will include tours of PDB structures in
UCSD's CAVE environment. Supported by private and
corporate sponsors, local colleges and universities, leading research institutes, and
hundreds of community and science organizations, SDSF showcases what is truly unique about
science in San Diego.

50 Years of Protein Structure Determination

The NIGMS has documented 50 years of advances in high-resolution protein structure
determination in an
interactive timeline. Beginning in 1958 with the publication of the first structure
in atomic detail, the timeline charts more than 25 advances over five decades. The
entries include brief descriptions, images and citations.

17-March-2009

PDB Archive Version 3.15 Released

A newly standardized and enhanced version of the entire PDB archive at
ftp://ftp.wwpdb.org has been released.

Files originally released before December 2, 2008 will follow PDB Format Version
3.15; files originally released after that date will follow Version 3.20. For
detailed file format documentation, please see www.wwpdb.org/docs.html.

Users who maintain local copies of the wwPDB FTP will have to download the entire archive.
Scripts to help in this process are available at www.wwpdb.org/downloads.html.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users
worldwide. This release includes improvements and enhancements to the data, including details about the
chemistry of the polymer and the ligands bound to it, biological assemblies, and binding sites of ligands
and metal ions. An overview
(PDF) is provided at the wwPDB website.

MyPDB is a new feature that regularly sends out emails when structures that match
customized queries are released.
The matching structures can be accessed directly from the email alerts. Users can
also log in to MyPDB to run stored searches at any time.

To sign up for MyPDB, users should register using the link at the top right of the RCSB PDB header.

Following registration, an activation link is sent in a confirmation email. After
activating the MyPDB account, users can log in at the top of the page.

Next, users can review currently saved queries and update MyPDB account information.
This page can also be accessed by clicking on the user name at the top of the page.

Saved MyPDB Queries can be keyword, sequence, ligand, and Advanced Searches.
To store a query in a profile, users should query the RCSB PDB website, such
as an Advanced Search for structures with Enzyme Commission Number 2.7.11.
After evaluating the query, the "Queries" tab in the left menu will temporarily
store the search. Selecting "Save Query to MyPDB" option from this tab will store
the search in MyPDB.

From the MyPDB page, users can click on the query name and query description to personalize them.

By default, the email notification is turned on. The "Next Scheduled Run" indicates when the query is next run.
Email alerts can be set to run weekly (Tuesday afternoon Pacific Time) or monthly (first Tuesday each month).

The email includes the customized query name and a list of PDB IDs and titles matching the query.
Clicking on the query name takes users to the results set at the RCSB PDB website; the results
can then be further refined, exported, or further explored. Each PDB ID links to the entry's
Structure Summary page.

Do you use protein crystal structure data? Ever wonder why things do not work out as you expect?
Are ligand strain energies unreasonably high? Does your drug candidate not appear to make the hydrogen bonds you expect?
Is that really a water molecule in the corner of a binding site?
Do you wonder why a side chain is in one position rather than another?

These questions all relate to the "quality" of the data you use.
How "good" are the protein structures that you use?
What's the error in atomic coordinates?
How might you know if something is just plain wrong?

Crystallography for Modelers will address these issues and offer
insight into state-of-the-art research into the quality, errors, and "gotchas"
in crystal structure data. Designed by active users of the data, the instructors
are experts from RCSB PDB team members, Rutgers researchers, and commercial
software developers. It is not an introductory course for crystallography
or modeling, but rather a down-and-dirty discussion of crystallographic data,
precision, accuracy, and possible errors.

Registration is for Day 1, Day 2 or both.
Day 2 will expand on Day 1 and offer an opportunity for hands-on learning.

Day 1: The process of crystal structure determination.
Insight into the workings of the PDB and how "PDB" files are generated.
Detailed examination of the extensive information (beyond coordinates)
available in data files and online, including ligand structures.
Proper interpretation of crystal structures, part one: accuracy,
precision, problems and errors (experimental, real, perceived).

Day 2: Proper interpretation of crystal structures, part two:
case studies with emphasis on ligand binding, position, conformation,
loops, and missing density. Software bridging modeling and crystallography.
Hands-on exercises in the concepts of the course with public and commercial
software. Software vendor showcase.

PDB Archive Version 3.15 to be Released March 17, 2009*

The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at
ftp://ftp.wwpdb.org with the March 17, 2009 update. *Please note the revised date.

Files originally released before December 2, 2008 will follow PDB
Format Version 3.15; files originally released after that date will
follow Version 3.20. For detailed file format documentation, please see
www.wwpdb.org/docs.html.

03-March-2009

PSI:Biology Phase Approved

In January 2009, the NIGMS Council approved the PSI's next 5-year plan of research, to be called
PSI:Biology. This new phase will concentrate on applying the technologies developed in the PSI
Pilot and Production phases to study a broader range of biological and biomedically relevant
scientific problems. More information can be found in the official
NIGMS news
release and at the PSI
SG Knowledgebase.

24-February-2009

Exhibition at the Biophysical Society Meeting

The RCSB PDB will participate in the exhibition at the 53rd Annual Meeting of the Biophysical Society
(February 28 - March 4) in Boston, Massachusetts. Staff will be available at booth #603 to answer
questions and to demonstrate the many deposition and query features available from
www.pdb.org. We hope to see you there!

(Click image to enlarge) Stop by the RCSB PDB exhibit booth for the latest RCSB PDB materials and more!

17-February-2009

PDB Archive Version 3.15 to be Released March 2009

The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at
ftp://ftp.wwpdb.org in March 2009.

Files originally released before December 2, 2008 will follow PDB
Format Version 3.15; files originally released after that date will
follow Version 3.20. For detailed file format documentation, please see
www.wwpdb.org/docs.html.

10-February-2009

Available only as a download, the poster
(31Mb) "Molecular Machinery: A Tour of the Protein Data Bank" features
illustrations of 75 select structures from the PDB, showing their
relative sizes at a scale of three million to one, and generally
describes their critical roles in the functions of living cells. A
2-sided, 8 1/2" x 11" quick
reference guide (5Mb) is also available.

Tools for Education

The General Education section of the RCSB PDB offers a variety of resources for
teachers and students interested in learning about protein and nucleic acid structures.

Accessible from the left hand menu, this section offers:

Looking at Structures: Through text, images, and interactive Jmols,
this feature intends to help researchers and educators get the most out of the PDB archive. Broad topics include
how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges
in exploring the archive.

Proteins in the Sea: An interactive kiosk at the The Sea of Genes exhibit at the Birch
Aquarium (La Jolla, CA) displayed information about specific proteins found in marine organisms--and in the PDB.
The Flash animation
used in the exhibit and a flyer (PDF)
describing it are available

Molecule of the Month: Each Molecule
of the Month installment includes an introduction to the structure and function of a particular molecule, a discussion
of the relevance of the molecule to human health and welfare, suggested additional readings and resources, and interactive views.

(Click
image to enlarge) A judge described how the models were scored with the team from Westfield.

(Click
image to enlarge) Annotators judged the protein models.

(Click
image to enlarge) The MATES Academy team built a portion of ribonuclease at the event.

Before the day of competition, teams build a model of the full ribonuclease structure based on PDB ID
1rta.
In this model, teams are encouraged to include "additions" that help tell the functional story
of ribonuclease.
They also provide an abstract/key that describes features highlighted in their model.

At the event itself, teams have 50 minutes to build a section of an assigned PDB structure and
answer questions about the structure, function, importance, and history of ribonuclease. For all
sections of the event, students are encouraged to use the
Molecule of the Month,
the PDB file, Jmol and the Structure Explorer page.

20-January-2009

Time-stamped Copies of PDB Archive Available via FTP

A time-stamped snapshot of the PDB archive (ftp.wwpdb.org) as of January 5, 2009 has
been added to ftp://snapshots.rcsb.org/. Snapshots of the PDB have been archived annually since 2004.
It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

The script at
ftp://snapshots.rcsb.org/rsyncSnapshots.sh
may be used to make a local copy of a snapshot or sections of the snapshot. The directory 20090105 includes
the?55,072?experimentally-determined coordinate files that were current at that time. Coordinate data are available in PDB, mmCIF, and XML formats.
The date and time stamp of each file indicates the last time the file was modified.

2009 NIGMS Workshop: Enabling Technologies for Structural Biology

The PSI and NIGMS have announced that the annual workshop
2009
NIGMS Workshop - Enabling Technologies for Structural Biology will be held March
4-6, 2009 at the NIH Natcher Conference Center in Bethesda, MD. This workshop will
focus on the technical challenges of protein structure determination and present the
latest technological and methodological innovations.

Many issues in structural genomics and structural biology are as applicable to the
individual bench scientist as they are to high-throughput research centers. The
preliminary program includes keynote presentations by Michael Rossmann and Frank
Raushel, six topical sessions, and a poster session. All classes of protein from
uncharacterized hypothetical proteins to membrane proteins and protein-protein
complexes will be discussed.

For further information regarding the 2009 NIGMS Workshop, online registration,
and abstract submission, visit
www.blsmeetings.net/2009workshop_enablingtechnologies.
The deadline for submitting an abstract is February 11, 2009, and selected abstracts will be invited to present their results.

13-January-2009

Newsletter Published

The winter 2009 edition offers tips for depositing multiple related structures and describes the release of PDB Archive
Version 3.15. Deposition and website statistics for 2008, the domain annotations in 3D view, the release of the 2008 Annual
Report, and the publication of a new resource for learning about PDB Data, called Looking at Structures, are described.

In this quarter's Education Corner, Bernadette Uzzi talks about protein structure-related courses available from
Brookhaven National Laboratory's Science Learning Center. In the Community Focus, Johannes Kirchmair and Gerhard Wolber
(University of Innsbruck) discuss their paper The Protein Data Bank (PDB), Its Related Services and Software Tools
as Key Components for In Silico Guided Drug Discovery, and more.

06-January-2009

Getting Started with the RCSB PDB Website

Not sure how to find what you're looking for on this website? The
Getting
Started page has been updated to help users access all of the data and related resources available
from the RCSB PDB. This introduction offers a Quick Start to using the website and explains the tabbed
navigation system and left hand menus.

For example, selecting each tab offers rich ways of exploring individual structures and search result sets.
The left-hand menus organize resources by topic. Teachers, for example, will be interested in the General Education
section of the website, while researchers depositing structures should look at the Deposit and Validate resources.

Other introductory resources include a narrated
tutorial that illustrates how to search, navigate, browse, generate reports, and visualize structures. The
Molecule of
the Month also provides a good introduction to the types of structures available in the PDB archive. And as
always, please let our help desk know if you have any questions